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- PDB-6yrx: Low-dose crystal structure of FAP at room temperature -

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Basic information

Entry
Database: PDB / ID: 6yrx
TitleLow-dose crystal structure of FAP at room temperature
ComponentsFatty acid Photodecarboxylase
KeywordsBIOSYNTHETIC PROTEIN / Low-dose / room temperature
Function / homology
Function and homology information


fatty acid photodecarboxylase / choline dehydrogenase activity / glycine betaine biosynthetic process from choline / chloroplast / flavin adenine dinucleotide binding / lyase activity / membrane
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / STEARIC ACID / Fatty acid photodecarboxylase, chloroplastic
Similarity search - Component
Biological speciesChlorella variabilis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSorigue, D. / Gotthard, G. / Blangy, S. / Nurizzo, D. / Royant, A. / Beisson, F. / Arnoux, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0021 France
CitationJournal: Science / Year: 2021
Title: Mechanism and dynamics of fatty acid photodecarboxylase.
Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / ...Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Cuine, S. / Doak, R.B. / Foucar, L. / Gorel, A. / Grunbein, M. / Hartmann, E. / Hienerwadel, R. / Hilpert, M. / Kloos, M. / Lane, T.J. / Legeret, B. / Legrand, P. / Li-Beisson, Y. / Moulin, S.L.Y. / Nurizzo, D. / Peltier, G. / Schiro, G. / Shoeman, R.L. / Sliwa, M. / Solinas, X. / Zhuang, B. / Barends, T.R.M. / Colletier, J.P. / Joffre, M. / Royant, A. / Berthomieu, C. / Weik, M. / Domratcheva, T. / Brettel, K. / Vos, M.H. / Schlichting, I. / Arnoux, P. / Muller, P. / Beisson, F.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4414
Polymers61,0871
Non-polymers1,3553
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-4 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.650, 105.650, 158.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11AAA-1124-

HOH

21AAA-1140-

HOH

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Components

#1: Protein Fatty acid Photodecarboxylase


Mass: 61086.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella variabilis (plant)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2D0TC92
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Na citrate, spermidine

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.87→88 Å / Num. obs: 65032 / % possible obs: 98.1 % / Redundancy: 4.278 % / Biso Wilson estimate: 36.072 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.124 / Χ2: 0.971 / Net I/σ(I): 7.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.87-24.2871.0640.98119460.4361.20899.7
2-2.164.190.6281.83109900.7050.71599.3
2.16-2.363.9410.3872.9397740.8570.44598.2
2.36-2.644.0570.2414.8287700.9360.27693.4
2.64-3.054.5650.158.3882510.9770.17199.8
3.05-3.734.5450.07615.7169480.9930.08699.5
3.73-5.254.5360.04724.3353650.9970.05498.2
5.25-884.4370.0427.1529880.9980.04693.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRU

6yru


Resolution: 1.87→47.181 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 3.759 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.18 3225 4.962 %
Rwork0.1544 --
all0.156 --
obs-64990 97.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.631 Å2
Baniso -1Baniso -2Baniso -3
1-1.073 Å20 Å20 Å2
2---1.282 Å20 Å2
3---0.209 Å2
Refinement stepCycle: LAST / Resolution: 1.87→47.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 93 340 4649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134459
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174125
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6496053
X-RAY DIFFRACTIONr_angle_other_deg1.4071.6029580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45121.598219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73215689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0291533
X-RAY DIFFRACTIONr_chiral_restr0.0780.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025082
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02930
X-RAY DIFFRACTIONr_nbd_refined0.2030.2802
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23805
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22162
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1380.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.26
X-RAY DIFFRACTIONr_nbd_other0.1990.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0830.210
X-RAY DIFFRACTIONr_mcbond_it2.6353.3592276
X-RAY DIFFRACTIONr_mcbond_other2.623.3572274
X-RAY DIFFRACTIONr_mcangle_it3.5875.0322848
X-RAY DIFFRACTIONr_mcangle_other3.5825.0312848
X-RAY DIFFRACTIONr_scbond_it4.2353.8582183
X-RAY DIFFRACTIONr_scbond_other4.2353.8612184
X-RAY DIFFRACTIONr_scangle_it6.5795.5563199
X-RAY DIFFRACTIONr_scangle_other6.5785.5593200
X-RAY DIFFRACTIONr_lrange_it8.23739.9884889
X-RAY DIFFRACTIONr_lrange_other8.16339.7144839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9180.3352410.334551X-RAY DIFFRACTION99.2132
1.918-1.9710.3192500.3054489X-RAY DIFFRACTION99.5797
1.971-2.0280.2752070.2814355X-RAY DIFFRACTION99.6723
2.028-2.0910.2572540.2484191X-RAY DIFFRACTION99.2188
2.091-2.1590.2512170.2314094X-RAY DIFFRACTION99.1947
2.159-2.2350.2472050.2193944X-RAY DIFFRACTION98.9506
2.235-2.3190.2372080.2023797X-RAY DIFFRACTION98.7183
2.319-2.4140.2251680.1883341X-RAY DIFFRACTION89.8822
2.414-2.5210.1841550.1813287X-RAY DIFFRACTION91.7377
2.521-2.6440.2381620.173435X-RAY DIFFRACTION99.7504
2.644-2.7870.1961630.1553242X-RAY DIFFRACTION99.7948
2.787-2.9560.1881740.1433073X-RAY DIFFRACTION99.7236
2.956-3.1590.1791570.1522862X-RAY DIFFRACTION99.7357
3.159-3.4120.1921260.1472740X-RAY DIFFRACTION99.7564
3.412-3.7370.1651180.1282474X-RAY DIFFRACTION99.0447
3.737-4.1780.1281190.12244X-RAY DIFFRACTION98.6639
4.178-4.8220.111180.0821977X-RAY DIFFRACTION98.1265
4.822-5.9010.109700.0951686X-RAY DIFFRACTION96.856
5.901-8.3270.117730.11274X-RAY DIFFRACTION94.6592
8.327-470.111400.128709X-RAY DIFFRACTION88.2214

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